Molecular Dynamics Simulations of Extracellular Enzyme-Mineral Interactions in Arctic Soils

Extracellular enzymes catalyze the hydrolysis of organic compounds, a critical initial step in the breakdown of complex soil organic matter. The ability of these enzymes to hydrolyze organic matter into simpler molecules is therefore an important kinetic control on microbial conversion of soil organic carbon into greenhouse gases. The Arctic environment is rapidly evolving – experiencing thawing of permafrost soils, increased thickening of the active layer into mineral soils, and more weathering. The purpose of this study is to investigate the association of extracellular enzymes with mineral surfaces and its implications on the enzymatic breakdown of complex organic carbon in Arctic active-layer environments. Using molecular dynamics simulations, we demonstrate that extracellular enzyme adsorption to mineral surfaces is dependent upon the charge characteristics of both the enzyme and the mineral surface. Additionally, the amount of structural deformation of the enzyme due to adsorption was dependent upon the structural characteristics of the enzyme itself. It is also shown that the potential for the enzyme to remain active upon adsorption can exist as the active site could remain accessible and flexible. The rest of the enzyme could decrease in flexibility, suggesting that adsorption may preserve these enzyme structures by making them more rigid. These simulations reveal the types of mechanisms behind enzyme-mineral adsorption, the importance of soil mineralogy for sorption mechanisms, and the influence of sorption on enzyme structure.